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A
GenTemplate
(
PLMD::cltools
)
Read
(
PLMD::generic
)
Ghost
(
PLMD::vatom
)
ReferenceArguments
(
PLMD
)
ABMD
(
PLMD::bias
)
GREX
(
PLMD
)
ReferenceAtoms
(
PLMD
)
Action
(
PLMD
)
Grid
(
PLMD
)
ReferenceConfiguration
(
PLMD
)
ActionAtomistic
(
PLMD
)
Group
(
PLMD::generic
)
ReferenceConfigurationOptions
(
PLMD
)
ActionOptions
(
PLMD
)
Gyration
(
PLMD::colvar
)
Communicator::Request
(
PLMD
)
ActionPilot
(
PLMD
)
H
Restart
(
PLMD::setup
)
ActionRegister
(
PLMD
)
Restraint
(
PLMD::bias
)
ActionSet
(
PLMD
)
Histogram
(
PLMD::analysis
)
RMSD
(
PLMD::colvar
)
ActionSetup
(
PLMD
)
Histogram
(
PLMD::vesselbase
)
RMSD
(
PLMD
)
ActionVolume
(
PLMD::multicolvar
)
HistogramBead
(
PLMD
)
RMSDBase
(
PLMD
)
ActionWithArguments
(
PLMD
)
I
MatrixSquareBracketsAccess::Row
(
PLMD
)
ActionWithInputVessel
(
PLMD::vesselbase
)
S
ActionWithValue
(
PLMD
)
IFile
(
PLMD
)
ActionWithVessel
(
PLMD::vesselbase
)
PathMSDBase::ImagePath
(
PLMD::colvar
)
SecondaryStructureRMSD
(
PLMD::secondarystructure
)
ActionWithVirtualAtom
(
PLMD
)
IMD
(
PLMD
)
SetupMolInfo
(
PLMD
)
AdjacencyMatrixAction
(
PLMD::multicolvar
)
Include
(
PLMD::generic
)
ShortcutVessel
(
PLMD::vesselbase
)
AdjacencyMatrixVessel
(
PLMD::multicolvar
)
Info
(
PLMD::cltools
)
SimpleCubic
(
PLMD::crystallization
)
AlphaBeta
(
PLMD::multicolvar
)
InterpolateBicubic
(
PLMD
)
SimpleMD
(
PLMD::cltools
)
AlphaRMSD
(
PLMD::secondarystructure
)
InterpolateCubic
(
PLMD
)
SimpleRMSD
(
PLMD
)
Analysis
(
PLMD::analysis
)
K
SingleDomainRMSD
(
PLMD
)
AnalysisWithLandmarks
(
PLMD::analysis
)
Sort
(
PLMD::function
)
Angle
(
PLMD
)
Kearsley
(
PLMD
)
SparseGrid
(
PLMD
)
Angle
(
PLMD::colvar
)
KernelFunctions
(
PLMD
)
SpathVessel
(
PLMD::mapping
)
Angles
(
PLMD::multicolvar
)
Keywords::KeyType
(
PLMD
)
Sprint
(
PLMD::multicolvar
)
AntibetaRMSD
(
PLMD::secondarystructure
)
Keywords
(
PLMD
)
Communicator::Status
(
PLMD
)
ArgumentOnlyDistance
(
PLMD
)
L
Steinhardt
(
PLMD::crystallization
)
AtomNumber
(
PLMD
)
Stopwatch
(
PLMD
)
Atoms
(
PLMD
)
LandmarkRegister
(
PLMD::analysis
)
StoreCentralAtomsVessel
(
PLMD::multicolvar
)
B
LandmarkSelectionBase
(
PLMD::analysis
)
StoreColvarVessel
(
PLMD::multicolvar
)
LandmarkSelectionOptions
(
PLMD::analysis
)
StoreDataVessel
(
PLMD::vesselbase
)
Between
(
PLMD::vesselbase
)
LatticeReduction
(
PLMD
)
StoreValueAndWeightVessel
(
PLMD::vesselbase
)
Bias
(
PLMD::bias
)
LessThan
(
PLMD::vesselbase
)
StoreValueVessel
(
PLMD::vesselbase
)
BiasRepresentation
(
PLMD
)
LinkCells
(
PLMD
)
StoreVectorsVessel
(
PLMD::crystallization
)
BiasValue
(
PLMD::bias
)
Load
(
PLMD::setup
)
Sum
(
PLMD::vesselbase
)
BiasWeight
(
PLMD
)
LOCAL_Q3
(
PLMD::crystallization
)
SwitchingFunction
(
PLMD
)
Bridge
(
PLMD::multicolvar
)
LOCAL_Q4
(
PLMD::crystallization
)
T
BridgeVessel
(
PLMD::vesselbase
)
LOCAL_Q6
(
PLMD::crystallization
)
C
LocalAverage
(
PLMD::multicolvar
)
Target
(
PLMD::function
)
LocalSteinhardt
(
PLMD::crystallization
)
TargetDist
(
PLMD
)
Cell
(
PLMD::colvar
)
Log
(
PLMD
)
Template
(
PLMD::colvar
)
Center
(
PLMD::vatom
)
LWalls
(
PLMD::bias
)
TensorChecks
(
PLMD
)
CH3Shifts
(
PLMD
)
M
TensorGeneric
(
PLMD
)
CInterpolation
(
PLMD
)
Tetrahedral
(
PLMD::crystallization
)
Citations
(
PLMD
)
Manual
(
PLMD::cltools
)
Time
(
PLMD::generic
)
ClassicalMultiDimensionalScaling
(
PLMD::analysis
)
ManyRestraintsBase
(
PLMD::manyrestraints
)
Stopwatch::Time
(
PLMD
)
ClassicalScaling
(
PLMD::analysis
)
Mapping
(
PLMD::mapping
)
Tools
(
PLMD
)
CLTool
(
PLMD
)
Matheval
(
PLMD::function
)
Torsion
(
PLMD
)
CLToolMain
(
PLMD
)
Matrix
(
PLMD
)
Torsion
(
PLMD::colvar
)
CLToolOptions
(
PLMD
)
MatrixSquareBracketsAccess
(
PLMD
)
Torsions
(
PLMD::multicolvar
)
CLToolRegister
(
PLMD
)
Max
(
PLMD::vesselbase
)
U
CLToolSumHills
(
PLMD::cltools
)
MDAtomsBase
(
PLMD
)
Colvar
(
PLMD
)
MDAtomsTyped
(
PLMD
)
Units
(
PLMD::setup
)
ColvarFake
(
PLMD::colvar
)
Mean
(
PLMD::vesselbase
)
Units
(
PLMD
)
COM
(
PLMD::vatom
)
MetaD
(
PLMD::bias
)
UWalls
(
PLMD::manyrestraints
)
Combine
(
PLMD::function
)
MetricRegister
(
PLMD
)
UWalls
(
PLMD::bias
)
Committor
(
PLMD::analysis
)
Min
(
PLMD::vesselbase
)
V
Communicator
(
PLMD
)
MolDataClass
(
PLMD
)
MatrixSquareBracketsAccess::Const_row
(
PLMD
)
MoleculeOrientation
(
PLMD::crystallization
)
Value
(
PLMD
)
Constant
(
PLMD::colvar
)
MolInfo
(
PLMD::setup
)
VectorChecks
(
PLMD
)
Communicator::ConstData
(
PLMD
)
Moments
(
PLMD::vesselbase
)
VectorGeneric
(
PLMD
)
ContactMap
(
PLMD::colvar
)
MoreThan
(
PLMD::vesselbase
)
VectorMean
(
PLMD::crystallization
)
Coordination
(
PLMD::colvar
)
MovingRestraint
(
PLMD::bias
)
VectorMultiColvar
(
PLMD::crystallization
)
CoordinationBase
(
PLMD::colvar
)
MPI_Comm
(
PLMD
)
Vessel
(
PLMD::vesselbase
)
CoordinationNumbers
(
PLMD::multicolvar
)
MPI_Datatype
(
PLMD
)
VesselOptions
(
PLMD::vesselbase
)
CopyAllFrames
(
PLMD::analysis
)
MPI_Request
(
PLMD
)
VesselRegister
(
PLMD::vesselbase
)
CS2Backbone
(
PLMD
)
MPI_Status
(
PLMD
)
Volume
(
PLMD::colvar
)
D
MultiColvar
(
PLMD::multicolvar
)
VolumeAround
(
PLMD::multicolvar
)
MultiColvarBase
(
PLMD::multicolvar
)
W
Communicator::Data
(
PLMD
)
MultiColvarFunction
(
PLMD::multicolvar
)
Debug
(
PLMD::generic
)
MultiDomainRMSD
(
PLMD
)
Stopwatch::Watch
(
PLMD
)
Density
(
PLMD::multicolvar
)
MultiReferenceBase
(
PLMD
)
WeightBase
(
PLMD
)
DHEnergy
(
PLMD::multicolvar
)
MultiRMSD
(
PLMD::colvar
)
WholeMolecules
(
PLMD::generic
)
DHEnergy
(
PLMD::colvar
)
N
WithCmd
(
PLMD
)
DihedralCorrelation
(
PLMD::multicolvar
)
X
Dipole
(
PLMD::colvar
)
NeighborList
(
PLMD
)
Distance
(
PLMD::colvar
)
NOE
(
PLMD::colvar
)
XDistances
(
PLMD::multicolvar
)
Distances
(
PLMD::multicolvar
)
NormalizedEuclideanDistance
(
PLMD
)
Z
DLLoader
(
PLMD
)
NumberOfLinks
(
PLMD::multicolvar
)
Atoms::DomainDecomposition
(
PLMD
)
O
ZpathVessel
(
PLMD::mapping
)
Driver
(
PLMD::cltools
)
f
DRMSD
(
PLMD
)
OFile
(
PLMD
)
DRMSD
(
PLMD::colvar
)
OptimalAlignment
(
PLMD
)
fio_iovec
(
PLMD::molfile
)
DumpAtoms
(
PLMD::generic
)
OptimalRMSD
(
PLMD
)
i
DumpDerivatives
(
PLMD::generic
)
OrientationSphere
(
PLMD::crystallization
)
DumpForces
(
PLMD::generic
)
P
PathMSDBase::imgOrderByDist
(
PLMD::colvar
)
DumpMultiColvar
(
PLMD::multicolvar
)
PathMSDBase::imgOrderBySimilarity
(
PLMD::colvar
)
DumpProjections
(
PLMD::generic
)
ParabetaRMSD
(
PLMD::secondarystructure
)
k
DynamicList
(
PLMD
)
Path
(
PLMD::mapping
)
E
PathBase
(
PLMD::mapping
)
kt
(
PLMD::cltools
)
PathMSD
(
PLMD::colvar
)
m
Energy
(
PLMD::colvar
)
PathMSDBase
(
PLMD::colvar
)
Ensemble
(
PLMD::function
)
Pbc
(
PLMD
)
md_atom
(
PLMD::molfile
)
EuclideanDistance
(
PLMD
)
PDB
(
PLMD
)
md_box
(
PLMD::molfile
)
Exception
(
PLMD
)
Piecewise
(
PLMD::function
)
md_file
(
PLMD::molfile
)
ExchangePatterns
(
PLMD
)
Plumed
(
PLMD
)
md_header
(
PLMD::molfile
)
External
(
PLMD::bias
)
PlumedMain
(
PLMD
)
md_ts
(
PLMD::molfile
)
F
PlumedMainInitializer
(
PLMD
)
molfile_atom_t
(
PLMD::molfile
)
PointWiseMapping
(
PLMD
)
molfile_graphics_t
(
PLMD::molfile
)
FakeFrame
(
PLMD
)
Position
(
PLMD::colvar
)
molfile_metadata_t
(
PLMD::molfile
)
Fccubic
(
PLMD::crystallization
)
Print
(
PLMD::generic
)
molfile_plugin_t
(
PLMD::molfile
)
IFile::Field
(
PLMD
)
ProbWeight
(
PLMD
)
molfile_qm_basis_t
(
PLMD::molfile
)
OFile::Field
(
PLMD
)
PropertyMap
(
PLMD::mapping
)
molfile_qm_hessian_t
(
PLMD::molfile
)
FileBase::FieldBase
(
PLMD
)
PropertyMap
(
PLMD::colvar
)
molfile_qm_metadata_t
(
PLMD::molfile
)
FileBase
(
PLMD
)
Q
molfile_qm_sysinfo_t
(
PLMD::molfile
)
FilesHandler
(
PLMD::function
)
molfile_qm_t
(
PLMD::molfile
)
FitToTemplate
(
PLMD::generic
)
Q3
(
PLMD::crystallization
)
molfile_qm_timestep_metadata
(
PLMD::molfile
)
FlexibleBin
(
PLMD
)
Q4
(
PLMD::crystallization
)
molfile_qm_timestep_t
(
PLMD::molfile
)
Flush
(
PLMD::generic
)
Q6
(
PLMD::crystallization
)
molfile_qm_wavefunction_t
(
PLMD::molfile
)
FuncPathMSD
(
PLMD::function
)
R
molfile_timestep_metadata
(
PLMD::molfile
)
FuncSumHills
(
PLMD::function
)
molfile_timestep_t
(
PLMD::molfile
)
Function
(
PLMD::function
)
Random
(
PLMD
)
molfile_volumetric_t
(
PLMD::molfile
)
FunctionVessel
(
PLMD::vesselbase
)
RandomExchanges
(
PLMD::generic
)
o
G
RDC
(
PLMD
)
FuncPathMSD::ordering
(
PLMD::function
)
MetaD::Gaussian
(
PLMD::bias
)
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